A large barge equipped with a crane sits on the Hudson River as pile driving has begun on the Tappan Zee Bridge (May 13, 2013) Photo Credit: Elizabeth Daza

The crews preparing to build the new $3.9 billion Tappan Zee Bridge are still determining the best methods to keep the waters of the Hudson River clear and clean as they dredge more than 950,000 cubic yards of tainted sludge from the river bottom in the late summer and early fall.

Dropping a two-foot-thick blanket of sand and stone on the 107-acre river-bottom trench cleared by the dredging, using clamshell shovels that keep a tight hold on the muck as it's pulled to the surface and digging slowly in order not to upset the torn-up river floor are among the strategies under consideration, said John Duschang, the environmental manager for Tappan Zee Constructors.

"Tappan Zee Constructors, in partnership with the New York State Thruway Authority, is taking extensive mitigation measures to lead the industry in environmental stewardship and to protect endangered species and other wildlife in the Hudson River," said Duschang.

The measures are key to making sure the dredging doesn't dirty the Hudson River with muck and silt that might harm the river's ecology and kill fish. Under the project's state environmental approvals, the color of the river water has to remain unchanged more than 500 feet from work.

"If you were driving over the current bridge and you saw brown water flowing from where they were dredging, that would be illegal," said Josh Verleun, an attorney at Riverkeeper, the Ossining-based environmental advocacy group that negotiated with state officials as they were applying for permits for the project.

Riverkeeper and Scenic Hudson unveiled a deal with Gov. Andrew M. Cuomo in March where the two groups agreed to drop their objections to the project while the state agreed to spend $11.5 million to restore wildlife habitat along the river.

The groups would make sure the state was sticking to the deal as well as living up to its commitments under its approvals, said Verleun.

"Riverkepper reserves our legal right to go out there and file a lawsuit ourselves to make sure they are following the permit," he said.

Tappan Zee Constructors is now testing soil samples to determine the extent of the toxic contamination in the river silt, said Duschang, adding that the toxicity would affect which facilities in Pennsylvania or New Jersey received and processed the sludge.

The testing is one of the many pre-work measures the company is undertaking before heavy work is permitted on the new span.

The bridge's environmental approvals allow Tappan Zee Constructors to dredge only between August and November in order to avoid the Atlantic and shortnose sturgeon spawning season.

The company expects to dredge this year and next, said Duschang.

Tappan Zee Constructors is also installing underwater barriers to protect the fish from noise and silt. Despite those precautions, as many as 86 of the endangered fish could perish in the project, according to state environmental approvals.

If and when construction on the bridge ends in 2018, as forecast, silt will naturaly return to the scarred river bottom at a rate of around a foot a year, said Verleun.

At that rate, the trench could take years to fill back up, said the Riverkeeper lawyer.

But at least Tappan Zee Constructors' plan involved far less dredging than the other two companies that bid for the project -- or 600,000 cubic yards less than the company that proposed the second-most amount of dredging, he said.

"We were very pleased with the project they chose as a winner," Verleun said. "It had a much smaller footprint than what was out there."